While being its own song, it incorporates the iconic notes from the Title theme. Most of the melody is performed on high-pitched flute-like synths, accompanied by very heavy drumbeats and dissonant electronic sounds. The track includes distorted crackling and static noises, possibly relating to Phazon since these sounds are heard in other music tracks associated with the substance. Aside from the Title Screen, it also plays in the Concept Gallery for the game.

A remix of the Metroid Prime Theme is used as the title theme of Metroid Prime Hunters: First Hunt. This version uses lower-quality instruments due to the limits of the Nintendo DS hardware. The result sounds "grittier" and more tense than the original theme. A similar arrangement can be found in the files of Metroid Prime Hunters, but is unused in the game itself.

The Metroid Prime Theme was partially remixed as Hunters, the intro movie and credits theme of Metroid Prime Hunters. Some of its notes are heard in the scene with Weavel, while the Title theme is heard in the scene with Samus Aran.

Metroid Prime Trilogy features the Metroid Prime Theme as one song that can be purchased in the Soundtrack Gallery. Its own title theme remixes the Title leitmotif with a high whistle, heavy drumbeats, and electronic static, most likely as a reference to the Metroid Prime Theme.